DYNATE (version 0.1)

Test_Leaf: Test_Leaf The function is used to generate Leaf P-values for case-control study. Users can input the leaf information through argument struct_map. If there is not leaf information e.g. struct_map=NULL, Test_Leaf will automatically construct leaf. Argument thresh_val specifies the leaf size constructed from the function. When the argument Gmat_case and Gmat_ctrl is null, Test_Leaf will automatically generate those matrices.

Description

Test_Leaf The function is used to generate Leaf P-values for case-control study. Users can input the leaf information through argument struct_map. If there is not leaf information e.g. struct_map=NULL, Test_Leaf will automatically construct leaf. Argument thresh_val specifies the leaf size constructed from the function. When the argument Gmat_case and Gmat_ctrl is null, Test_Leaf will automatically generate those matrices.

Usage

Test_Leaf(snp_dat = NULL, thresh_val = 10, covars = NULL, teststat = "FET")

Value

a dataframe of rejected leafs with snp information.

Arguments

snp_dat

an optional data frame containing patients mutation information. If snp_dat=NULL, the mutation information should be taken from Gmat_case, Gmat_ctrl and glm_input. See vignettes for detail.

thresh_val

a positive integer for leaf size.

covars

an optional vector about the name of covariates to be considered in the fitting process. Should be NULL (default) or a character vector.

teststat

the statistic used to derive p-value. Must be one of "FET" (default) or "score".

Examples

data("snp_dat")

# Set leaf size M
M <- 5

#Construct leaves and generate leaf p-value.
p.leaf <- Test_Leaf(snp_dat=snp_dat,thresh_val=M)
summary(p.leaf)